Package org.openscience.cdk.isomorphism

Class VentoFoggia

java.lang.Object
org.openscience.cdk.isomorphism.Pattern
org.openscience.cdk.isomorphism.VentoFoggia
public final class VentoFoggia extends Pattern
A structure pattern which utilises the Vento-Foggia (VF) algorithm [Cordella Luigi P et. al.. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. 2004. 26]. Find and count the number molecules which contain the query substructure. 
 IAtomContainer query   = ...;
 Pattern        pattern = VentoFoggia.findSubstructure(query);

 int hits = 0;
 for (IAtomContainer m : ms)
     if (pattern.matches(m))
         hits++;
Finding the matching to molecules which contain the query substructure. It is more efficient to obtain the match(org.openscience.cdk.interfaces.IAtomContainer) and check it's size rather than test if it Pattern.matches(org.openscience.cdk.interfaces.IAtomContainer). These methods automatically verify stereochemistry. 

 IAtomContainer query   = ...;
 Pattern        pattern = VentoFoggia.findSubstructure(query);

 int hits = 0;
 for (IAtomContainer m : ms) {
     int[] match = pattern.match(m);
     if (match.length > 0)
         hits++;
 }
Author:
John May
Belongs to CDK module:
isomorphism

  • Method Details

    • match

      public int[] match(IAtomContainer target)
      Find a matching of this pattern in the target. If no such order exist an empty mapping is returned. Depending on the implementation stereochemistry may be checked (recommended). 
      
 Pattern        pattern = ...; // create pattern
 for (IAtomContainer m : ms) {
     int[] mapping = pattern.match(m);
     if (mapping.length > 0) {
         // found mapping!
     }
 }
      Specified by:
      match in class Pattern
      Parameters:
      target - the container to search for the pattern in
      Returns:
      the mapping from the pattern to the target or an empty array

    • matchAll

      public Mappings matchAll(IAtomContainer target)
      Find all mappings of this pattern in the target. Stereochemistry should not be checked to allow filtering with Mappings.stereochemistry(). 
       Pattern pattern = Pattern.findSubstructure(query);
 for (IAtomContainer m : ms) {
     for (int[] mapping : pattern.matchAll(m)) {
         // found mapping
     }
 }
      Using the fluent interface (see Mappings) we can search and manipulate the mappings. Here's an example of finding the first 5 mappings and creating an array. If the mapper is lazy other states are simply not explored. 
       // find only the first 5 mappings and store them in an array
 Pattern pattern  = Pattern.findSubstructure(query);
 int[][] mappings = pattern.matchAll(target)
                           .limit(5)
                           .toArray();
      Specified by:
      matchAll in class Pattern
      Parameters:
      target - the container to search for the pattern in
      Returns:
      the mapping from the pattern to the target
      See Also:

    • findSubstructure

      public static Pattern findSubstructure(IAtomContainer query)
      Create a pattern which can be used to find molecules which contain the query structure.
      Parameters:
      query - the substructure to find
      Returns:
      a pattern for finding the query

    • findIdentical

      public static Pattern findIdentical(IAtomContainer query)
      Create a pattern which can be used to find molecules which are the same as the query structure.
      Parameters:
      query - the substructure to find
      Returns:
      a pattern for finding the query

    • findSubstructure

      public static Pattern findSubstructure(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
      Create a pattern which can be used to find molecules which contain the query structure.
      Parameters:
      query - the substructure to find
      atomMatcher - how atoms are matched
      bondMatcher - how bonds are matched
      Returns:
      a pattern for finding the query

    • findIdentical

      public static Pattern findIdentical(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
      Create a pattern which can be used to find molecules which are the same as the query structure.
      Parameters:
      query - the substructure to find
      atomMatcher - how atoms are matched
      bondMatcher - how bonds are matched
      Returns:
      a pattern for finding the query